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Entry
Database: PDB / ID: 3c1l
TitleCrystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution
ComponentsPutative antioxidant defense protein Mlr4105
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
AhpD-like / Uncharacterised peroxidase-related / Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Mlr4105 protein
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD, molecular replacement / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative antioxidant defense protein (NP_105057.1) from Mesorhizobium loti at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative antioxidant defense protein Mlr4105
B: Putative antioxidant defense protein Mlr4105
C: Putative antioxidant defense protein Mlr4105
D: Putative antioxidant defense protein Mlr4105
E: Putative antioxidant defense protein Mlr4105
F: Putative antioxidant defense protein Mlr4105
G: Putative antioxidant defense protein Mlr4105
H: Putative antioxidant defense protein Mlr4105
I: Putative antioxidant defense protein Mlr4105
J: Putative antioxidant defense protein Mlr4105
K: Putative antioxidant defense protein Mlr4105
L: Putative antioxidant defense protein Mlr4105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,15338
Polymers252,46412
Non-polymers2,68826
Water13,169731
1
A: Putative antioxidant defense protein Mlr4105
B: Putative antioxidant defense protein Mlr4105
C: Putative antioxidant defense protein Mlr4105
D: Putative antioxidant defense protein Mlr4105
E: Putative antioxidant defense protein Mlr4105
F: Putative antioxidant defense protein Mlr4105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,93022
Polymers126,2326
Non-polymers1,69816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
MethodPISA
2
G: Putative antioxidant defense protein Mlr4105
H: Putative antioxidant defense protein Mlr4105
I: Putative antioxidant defense protein Mlr4105
J: Putative antioxidant defense protein Mlr4105
K: Putative antioxidant defense protein Mlr4105
L: Putative antioxidant defense protein Mlr4105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,22316
Polymers126,2326
Non-polymers99110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.690, 68.060, 266.830
Angle α, β, γ (deg.)90.000, 95.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21B
31C
41D
51E
61F
71A
81H
91I
101J
111K
121L

NCS domain segments:

Ens-ID: 1 / End label comp-ID: ARG / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEGG1 - 1872 - 188
23GLYBB3 - 1874 - 188
33GLYCC3 - 1874 - 188
44LYSDD4 - 1875 - 188
54LYSEE4 - 1875 - 188
64LYSFF4 - 1875 - 188
74LYSAA4 - 1875 - 188
84LYSHH4 - 1875 - 188
93GLYII3 - 1874 - 188
103GLYJJ3 - 1874 - 188
113GLYKK3 - 1874 - 188
123GLYLL3 - 1874 - 188

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Components

#1: Protein
Putative antioxidant defense protein Mlr4105


Mass: 21038.684 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_105057.1, mlr4105 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98ES4
#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT USED FOR REFINEMENT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...1. THE CONSTRUCT USED FOR REFINEMENT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 1-187 OF THE TARGET SEQUENCE. 2. THE CRYSTAL USED FOR SAD PHASING WAS FROM AN N-TERMINAL TRUNCATED CONSTRUCT. THE CONSTRUCT USED THE SAME TEV-CLEAVED TAG FOLLOWED BY RESIDUES 34-187 OF THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3547.66TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.50 ANGSTROM SAD DATA COLLECTED FROM A CRYSTAL IN SPACE GROUP P3121 WERE USED TO PHASE AND TRACE AN INITIAL MODEL. THIS MODEL WAS THEN USED FOR MOLECULAR REPLACEMENT AGAINST A CRYSTAL IN SPACE GROUP P21 THAT DIFFRACTED TO 2.0 ANGSTROMS. REFINEMENT WAS AGAINST THE AMPLITUDES FROM THE P21 CRYSTAL. NOTE THAT THE TWO CRYSTALS ARE FROM SLIGHTLY DIFFERENT PROTEIN CONSTRUCTS. THE P3121 SAD PHASING CRYSTAL IS OF A TRUNCATED CONSTRUCT (RESIDUES 34-187), WHILE THE P21 CRYSTAL USED FOR REFINEMENT WAS FROM THE FULL LENGTH CONSTRUCT, RESIDUES 1-187.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8NANODROP, 20.0% PEG 6000, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.2NANODROP, 0.2M NaCl, 50.0% PEG 200, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91837
SYNCHROTRONAPS 23-ID-D20.97942
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 11, 2007Flat mirror (vertical focusing)
MARMOSAIC 300 mm CCD2CCDAug 19, 2007Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Si(111) Double crystalSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979421
ReflectionResolution: 2→29.814 Å / Num. obs: 138837 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.909 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.3541.65368127371,241.9
2.07-2.150.3041.97970166601,255.3
2.15-2.250.232.513005240911,275.4
2.25-2.370.1863.320920297321,294.6
2.37-2.520.1454.222565301671,295.9
2.52-2.710.1175.222541294001,296.7
2.71-2.990.0856.923833307361,296.4
2.99-3.420.05510.323314299121,297
3.42-4.30.03714.623186299211,296.8
4.3-29.8140.02816.723505295611,294.6

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Phasing

PhasingMethod: SAD, molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0066refinement
PHENIXrefinement
MolProbity3beta29model building
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
MOSFLMdata reduction
XSCALEdata scaling
SCALAdata scaling
SHARPphasing
MOLREPphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2→29.814 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.244 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CHAIN L, PARTICULARLY THE FIRST 60 RESIDUES, IS LOCATED IN WEAK DENSITY. 5. PEG AND CL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RAMACHANDRAN OUTLIERS ARE IN POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 6959 5 %RANDOM
Rwork0.171 ---
obs0.174 138822 87.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.04 Å2
2--0.25 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16600 0 176 731 17507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02217097
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211602
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.97223039
X-RAY DIFFRACTIONr_angle_other_deg0.992328145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84652178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99523.542751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.072152827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8615135
X-RAY DIFFRACTIONr_chiral_restr0.0870.22581
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023533
X-RAY DIFFRACTIONr_mcbond_it1.466310907
X-RAY DIFFRACTIONr_mcbond_other0.71134391
X-RAY DIFFRACTIONr_mcangle_it2.248517255
X-RAY DIFFRACTIONr_scbond_it4.22386190
X-RAY DIFFRACTIONr_scangle_it5.879115776
Refine LS restraints NCS

Ens-ID: 1 / Number: 2091 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1GMEDIUM POSITIONAL0.390.5
2BMEDIUM POSITIONAL0.40.5
3CMEDIUM POSITIONAL0.380.5
4DMEDIUM POSITIONAL0.320.5
5EMEDIUM POSITIONAL0.330.5
6FMEDIUM POSITIONAL0.30.5
7AMEDIUM POSITIONAL0.410.5
8HMEDIUM POSITIONAL0.310.5
9IMEDIUM POSITIONAL0.360.5
10JMEDIUM POSITIONAL0.380.5
11KMEDIUM POSITIONAL0.430.5
12LMEDIUM POSITIONAL0.530.5
1GMEDIUM THERMAL1.212
2BMEDIUM THERMAL1.142
3CMEDIUM THERMAL1.192
4DMEDIUM THERMAL1.152
5EMEDIUM THERMAL1.112
6FMEDIUM THERMAL1.042
7AMEDIUM THERMAL1.22
8HMEDIUM THERMAL1.032
9IMEDIUM THERMAL1.142
10JMEDIUM THERMAL1.092
11KMEDIUM THERMAL0.892
12LMEDIUM THERMAL0.832
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 264 -
Rwork0.242 5071 -
all-5335 -
obs--45.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89260.11250.64951.2116-0.20181.46820.0201-0.0970.14760.13080.0063-0.0325-0.14960.0645-0.0265-0.1506-0.00290.0256-0.1648-0.0355-0.112514.804823.349557.4757
21.3449-0.42150.15312.3747-0.06281.3951-0.03370.0040.22130.05250.0602-0.2095-0.28330.1703-0.0265-0.1411-0.05580.0229-0.0995-0.0419-0.074428.12428.202741.3535
31.9890.0411-0.86881.13750.04051.5222-0.0454-0.0395-0.18120.09470.00490.01320.1495-0.05160.0405-0.154-0.0066-0.0179-0.1750.0132-0.1271-0.6876-1.482653.5917
41.954-0.4793-0.1691.81540.76471.9949-0.03530.1055-0.25180.0464-0.02630.18970.2684-0.15570.0617-0.1597-0.03240.0083-0.11110.0055-0.122-11.3634-2.11134.3328
51.6047-0.03140.45111.2171-0.12811.57940.02640.2241-0.0556-0.2145-0.0289-0.04680.05130.02230.0026-0.07880.00030.0319-0.1044-0.0161-0.13865.73756.1211.5172
61.99740.15320.38071.4270.03971.4727-0.01920.31580.1273-0.31210.0102-0.1081-0.26630.09810.009-0.0072-0.02390.0288-0.09410.0162-0.108115.424325.400114.5343
72.5567-0.4484-0.43121.05060.32341.8680.01920.0535-0.3078-0.0774-0.02510.0510.20840.07120.0058-0.10860.0043-0.0361-0.1663-0.0215-0.037147.546434.39381.3987
82.84170.0576-0.27712.058-0.61312.131-0.1292-0.3625-0.38970.08890.0932-0.19510.32610.22220.036-0.08730.0515-0.0329-0.02090.0192-0.025560.706735.511698.6736
92.0330.26430.3341.79770.11071.43050.01030.12480.1963-0.14370.00440.1181-0.1085-0.0748-0.0147-0.13990.0119-0.001-0.13110.0056-0.108431.615558.807577.3727
101.68810.0249-0.20822.5523-0.26881.6772-0.0229-0.13170.19610.09010.07160.1585-0.2186-0.143-0.0487-0.11350.0198-0.002-0.02-0.0418-0.104421.107665.745295.4402
112.988-0.8307-0.04752.10690.34241.4713-0.2563-0.87040.37810.47130.2468-0.2305-0.15880.14910.00950.14110.0691-0.1130.2896-0.1347-0.028238.532765.4774119.1444
124.3258-2.4254-0.22062.89570.05361.3877-0.5766-1.2235-0.23260.88210.5680.13380.13770.10480.00860.25570.20930.01240.47270.1108-0.072247.454645.3355122.1956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1875 - 188
2X-RAY DIFFRACTION2BB3 - 1874 - 188
3X-RAY DIFFRACTION3CC3 - 1874 - 188
4X-RAY DIFFRACTION4DD4 - 1875 - 188
5X-RAY DIFFRACTION5EE4 - 1875 - 188
6X-RAY DIFFRACTION6FF4 - 1875 - 188
7X-RAY DIFFRACTION7GG1 - 1872 - 188
8X-RAY DIFFRACTION8HH4 - 1875 - 188
9X-RAY DIFFRACTION9II3 - 1874 - 188
10X-RAY DIFFRACTION10JJ3 - 1874 - 188
11X-RAY DIFFRACTION11KK3 - 1874 - 188
12X-RAY DIFFRACTION12LL3 - 1874 - 188

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